Building a cohesive bioinformatics classroom: implementation of

wireless sharing technology in a large scale-up of SEA-PHAGES

introductory biology lab

Welkin Pope

Biological Sciences

July 1 2015

Seaphages.org

Brussow and Hendrix, 2002

Phagesdb.org

Fall semester: Phage DiscoveryFind phage—purify—amplify—extract DNA—characterize

(2x per week, 2 hour classes)

– Design an experiment with hypothesis, controls, etc

– Keep lab notebooks– Scientific notation– Serial dilutions– Use micropipettors– Sterile technique– Scientific presentation

(Poster, Figures)

• Spring semester: Bioinformatics• Annotate genome—comparative genomics—

further explorations (2x per week, 2 hour classes)

– Design experiments in bioinformatics (computer programs as experiments)

– Keep electronic lab notebook– Further develop presentation skills– Read and write primary literature (genome

announcements)– Generate, plan and execute multi-experiment project

in phage biology using what they have learned.

• >Anaya Complete Sequence, 60835 bp, including 11 bp 3' overhang (CTCGTAGGCAT), Cluster K1

• AGGCACCTTTCTCTCCCCAGCATTTTTTTCCAAGCCGATTCAGCGTTTTT

• CCACGCCCGACCAGCACAGGAGCAACCAATGCACATGACCGAATCCGAAC

• CGACTGCGCGCGTGTGGGCGTTCGAGGATCAGCGCGACCGCGCGGTGCGC

• GAGCAATCAATGCACATCGCGTTGAAGGCCGCCGACATCGTGGGTCTCGG

• CGACGTGACGCTGATCGAGGCGGCCGACAAGATCGCCGATTTCATCCTCG

• ACGGCAAGGTCGACCGGCGCCCCGACGCTGAGCGGAGCCCCGAATGATGA

• CGCCCGCCGAGCGTCTCGCCGCGCAGCGCGAGGCCCTCGACAAGCACGAG

• TGGACCGAGGTCGAGGGCGACCTCACGCCGATCACGCTGCACTGTCTGGT

• CGCTATTGGCGAGGTGCTCGTCGAGCTGAACGCCCGGCAGGCCCGCCAGG

• AGGCCGCAGCGATGGGCGCCCCGTCGTGAGCCCGGTCGTCGGCGTCGTGT

• CGCGCACGCTCGACAGCGCGGCCCGGCTCGCCCGCGCGCTGAACGTGGCT

• CGCACCGTTCCAATGAGCGTGCCGTCGATCAAGCAGGGGCACGGCCGCGG

• GTTCAGTTTCGACGCCGTGATCGTCGACGACGAGGTGATGCCGCTCGATG

• ACTGTGTGCTCGGCACGTTGGCCCCGGCGATGCACGCTCACGGCGGAAAG

• ATGTACGCGGTTCGGGAGGTTGAGCTGTGACCCCGACTGTCGGCCGCATC

• GTTCATTACCAGTCTTACGGCACGCCCGGCGGCGAGCACCTGCCTGAGCC

• CCGCGCCGCGATCGTCACGGCCGTGCTCGGCGGTGGCGTCGTGAGCCTGT

• GTGTGCTCAACCCGTCGGGGCTGTTTTTCAACGAGTCCGTGCGCCAGGCC

• GACGAGCCGACGCCGGGCCGCTGGAATTGGCCGCCCCGCAACTGATCTAG

• CGCGCGTAGCCCAACCGACGGATAGAGGCGGCTGGTAATTCGGCGTCAAC

• GTGCCGGGCCTCGTCAGCCCGGCCGCGCGCAAATGGGTGTGTAGCTCAAT

• TGGCAGAGCAGCGGTCTCCAAAGCCGCCGGTTGCACGTTCGAGTCGTGCC

• GCGCCCGCTTCCACACCGGCTAACCGCCGGCGATCCGCATTCCCGCACGT

• CAACGCCACGAAAGGCCGTTTTGAGCTAACACGGCACCTCAACACACCAG

• GAGATATGACCATGCGCGCACCCGCTACCGCCGAGGTTCCTTGCCCGGCC

• TGCGGCGAGCCGATCACGCTCGCCCTTGGCTTTGAGCTGGCCGAGCCTGA

• GCCCGGCGCCACGACTGCCCCAATGTTCGTGAGGCCGCTCGACATTGCAG

• AGCGCGCGCAGGAGCACGGCGAGGTGTGCCCGGTGTGGTCAGGCGGTGGC

• CGCGATGACTGACGGCAAGCTCGACCGGCTCGGCGAGCTGCGACGGTTGC

• ACGAGCGCATCTCGT…..

R H L S L P S I F F Q A I S A F F H T R P A Q E Q P M D M T E S A P

G T F L S P A F F S K P F Q R F S T P D Q H R S N Q W T * P N P H

A P F S P Q H F F P S H F S V F P H P T S T G A T N G H D R I R T

1 AGGCACCTTTCTCTCCCCAGCATTTTTTTCCAAGCCATTTCAGCGTTTTTCCACACCCGACCAGCACAGGAGCAACCAATGGACATGACCGAATCCGCAC

....:....|....:....|....:....|....:....|....:....|....:....|....:....|....:....|....:....|....:....|

TCCGTGGAAAGAGAGGGGTCGTAAAAAAAGGTTCGGTAAAGTCGCAAAAAGGTGTGGGCTGGTCGTGTCCTCGTTGGTTACCTGTACTGGCTTAGGCGTG

Y A G K E G W C K K G L W K L T K G C G V L V P A V L P C S R I R V

L C R E R G L M K K W A M E A N K W V R G A C S C G I S M V S D A

P V K R E G A N K E L G N * R K E V G S W C L L L W H V H G F G C

T A R V W A F E D Q R D R A V R E Q S M H I A L R Q A D S V G I G

R L R A C G R S R I S A T A R C A S N Q C T S R C A R P T A W V S A

D C A R V G V R G S A R P R G A R A I N A H R A A P G R Q R G Y R

101 CGACTGCGCGCGTGTGGGCGTTCGAGGATCAGCGCGACCGCGCGGTGCGCGAGCAATCAATGCACATCGCGCTGCGCCAGGCCGACAGCGTGGGTATCGG

....:....|....:....|....:....|....:....|....:....|....:....|....:....|....:....|....:....|....:....|

GCTGACGCGCGCACACCCGCAAGCTCCTAGTCGCGCTGGCGCGCCACGCGCTCGTTAGTTACGTGTAGCGCGACGCGGTCCGGCTGTCGCACCCATAGCC

S Q A R T P T R P D A R G R P A R A I L A C R A A G P R C R P Y R

G V A R T H A N S S * R S R A T R S C D I C M A S R W A S L T P I P

R S R A H P R E L I L A V A R H A L L * H V D R Q A L G V A H T D

D L T V I E A A D K I A A F I L D G K V D R R P D A E R S P E * *

T * P * S R R P T R S P L S S S T A R S T G A P T L S G A P N D D

R L D R D R G G R Q D R R F H P R R Q G R P A P R R * A E P R M M T

201 CGACTTGACCGTGATCGAGGCGGCCGACAAGATCGCCGCTTTCATCCTCGACGGCAAGGTCGACCGGCGCCCCGACGCTGAGCGGAGCCCCGAATGATGA

....:....|....:....|....:....|....:....|....:....|....:....|....:....|....:....|....:....|....:....|

GCTGAACTGGCACTAGCTCCGCCGGCTGTTCTAGCGGCGAAAGTAGGAGCTGCCGTTCCAGCTGGCCGCGGGGCTGCGACTCGCCTCGGGGCTTACTACT

R S S R S R P P R C S R R K * G R R C P R G A G R R Q A S G R I I

S K V T I S A A S L I A A K M R S P L T S R R G S A S R L G S H H

A V Q G H D L R G V L D G S E D E V A L D V P A G V S L P A G F S S

12

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0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Inaugural SEA-PHAGES class at Pitt, 2012-2013

Challenges: Multi-year large scale-up from 1 section to 15(?)

• Maintain the quality of the student experience and the scientific research with non-expert instructors and many many MANY more students!

• Maintain the sense of community in the course

• Logistics: how do we fit all those lab sections into the space available?

Last year’s solutions (increased from 1 to 5 sections)

• Added 1 lecture per week, all students attend.

• Increased number of UTAs (used alumni)

• Decreased length of lab classes (1hr 20min each; still 2x per week)

• Students used own laptops for bioinformatics

Bioinformatics Challenges

Students work in groups to annotate different bacteriophage genomes.

• Concepts are more abstract than in fall semester

• More room for interpretation in making final decisions

• Genomes are all different

– May or may not be similar to previously annotated genomes

– May or may not be similar to others in class

Annotation requires application of “guiding principles” of bacteriophage annotation and careful analysis of (sometimes conflicting) data from multiple computer programs: DNA Master, Phamerator, Starterator, GeneMark, Glimmer, BLAST, HHPred, and others.

Goals for Course Transformation:*Decrease amount of course time spent doing annotations *Expose more students to genomes and genome features *Build sense of cross-section community

Problem: How to share data live during class for discussion/demonstration?

Tried: Box, Power Point, Google Slides, email….All of these require either forethought or wasting class time for file transfers.

• Solution:

ClickShares!

– Wireless receiver connected to projector; can connect any computer via USB; or can connect tablet/smart phone

– Can show up to four screens at once.

Assessment

• Pre- and post- survey

• Student interviews during implementation

• Pre- and post- measurement of time on task

• Survey designed with the assistance of DrDavid Hanuaer, IUP, and lead SEA-PHAGES assessment coordinator; uses validated tools.

Pre-survey

• Administered spring 2015, voluntary

• 38 out of 82 students answered

• Three questions: – Where did students get help/feedback on

annotations?

– How familiar did they feel with other groups’ annotations?

– How comfortable were they with the annotation process, including genome features that were not present in all genomes?

1. To what degree did you receive feedback on your annotations from:

# Question Not At All Occasionally Frequently Total Responses

Mean

1 Your course instructor

2 11 25 38 2.61

2 Your TAs 2 20 16 38 2.37

3 Students in your group

3 10 25 38 2.58

4 Other students in your lab section section

15 19 4 38 1.71

5 Students that are in the SEA-PHAGES but not in your lab section

23 13 2 38 1.45

1. To what degree did you receive feedback on your annotations from:

Statistic Your course instructor

Your TAs Students in your group

Other students in your lab section section

Students that are in the SEA-PHAGES but not in your lab section

Min Value 1 1 1 1 1

Max Value 3 3 3 3 3

Mean 2.61 2.37 2.58 1.71 1.45

Variance 0.35 0.35 0.41 0.43 0.36

Standard Deviation

0.59 0.59 0.64 0.65 0.60

Total Responses 38 38 38 38 38

2. Please rate your familiarity with other student groups annotations

# Question I know nothing about the annotations of other students

I have seen some of the annotations but I am not familiar with them

I have seen some of the annotations but I am not really sure I am familiar with them

I have seen the annotations of other students and have some familiarity with them

I am completely familiar with other students annotations

Total Responses

Mean

1 To what degree are you familiar with the annotations of other groups of students

1 7 13 16 1 38 3.24

2. Please rate your familiarity with other student groups annotations

Statistic To what degree are you familiar with the annotations of other groups of students

Min Value 1

Max Value 5

Mean 3.24

Variance 0.78

Standard Deviation 0.88

Total Responses 38

3. Rate the degree to which you agree or disagree with the followingstatements

Question Strongly Disagree

Disagree Neither Agree nor Disagree

Agree Strongly Agree

Total Responses

Mean

I feel confident that I know how to apply the guiding principles to my phage genome annotation

0 1 1 22 14 38 4.29

I feel comfortable assigning functions to phage genes

0 0 4 23 11 38 4.18

I feel comfortable annotating a tRNA

6 12 12 6 2 38 2.63

I feel comfortable annotating a programmed translational frame shift

7 10 8 11 2 38 2.76

I can easily describe what is specific about my phage genome that isn't found in other phage genomes in this course

0 4 2 20 12 38 4.05

3. Rate the degree to which you agree or disagree with the followingstatements

Statistic I feel confident that I know how to apply the guiding principles to my phage genome annotation

I feel comfortable assigning functions to phage genes

I feel comfortable annotating a tRNA

I feel comfortable annotating a programmed translational frame shift

I can easily describe what is specific about my phage genome that isn't found in other phage genomes in this course

Min Value 2 3 1 1 2

Max Value 5 5 5 5 5

Mean 4.29 4.18 2.63 2.76 4.05

Variance 0.43 0.37 1.21 1.48 0.81

Standard Deviation

0.65 0.61 1.10 1.22 0.90

Total Responses 38 38 38 38 38

Additional thoughts?

• Incorporate grades?

• Adjunct instructors and “expert” UTAs

• Replace lecture with online modules?

• Open lab hours?